Anthropogenic-induced changes in nutrient ratios have increased the susceptibility of large temperate lakes to several effects of rising air temperatures and the resulting heating of water bodies. First, warming leads to stronger thermal stratification, thus impeding natural complete water turnover (holomixis), which compensates for oxygen deficits in the deep zones. Second, increased water temperatures and nutrient concentrations can directly favour the growth of harmful algae. Thus, lake-restoration programmes have focused on reducing nutrients to limit toxic algal blooms. Here we present evidence that the ubiquitous harmful cyanobacterium Planktothrix rubescens has become the dominant species in a large lake during the past four decades, although the phosphorus content of the ecosystem decreased fivefold.